GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Magnetospirillum magneticum AMB-1

Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate WP_011385763.1 AMB_RS17210 molybdenum import ATP-binding protein ModC

Query= TCDB::Q88P35
         (384 letters)



>NCBI__GCF_000009985.1:WP_011385763.1
          Length = 363

 Score =  146 bits (369), Expect = 8e-40
 Identities = 103/304 (33%), Positives = 160/304 (52%), Gaps = 31/304 (10%)

Query: 23  DIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGGAI------LIDEQDVSGMSPKD 76
           D++LS   G    L G SG GK++++N +AGL +   G+I      L D +    + P+ 
Sbjct: 16  DVRLSAGPG-VTALYGRSGSGKTSVINMVAGLSRPDEGSISVDGRVLFDSRSGIDLPPEA 74

Query: 77  RDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVAKLLQIEHLLARKPAQL 136
           R +  VFQ + L+P +SVR N+EFG K+  LP A   + + +V +LL IE LL R+PA+L
Sbjct: 75  RRLGYVFQEHRLFPHLSVRGNLEFGQKL--LPSAERTQSLDKVVELLGIESLLDRRPAKL 132

Query: 137 SGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQ 196
           SGG++QRVA+GRAL   P+I L DEPL+ LD   + E+   +  + +R     +YV+H  
Sbjct: 133 SGGEKQRVAIGRALLASPRILLMDEPLAALDPARKAEVLPFIAQLARRFSVPILYVSHSM 192

Query: 197 IEAMTLGDKVAVMKDGIIQQFGTPQQIYNDP----------ANQFVASFIGSPPMNFIPV 246
            E + L D +A+M  G +   G  + +  DP          A   + + + S    F   
Sbjct: 193 DEVLRLADTLALMDGGKVAASGPLESLMGDPGLRPLTGRYEAGAVIGAVVSSHDSGFGIS 252

Query: 247 RLARQDGRLLALLDSGQARCELPLG-EAADALEGREIILGIR-PEQIALGAADGNGLPAI 304
           RLA   G L+        R ELP+G +    +  R++ + I  P+++++     N LPAI
Sbjct: 253 RLAFDGGTLIV------GRSELPVGAKVRLRIHARDVAIAIEPPDRVSI----RNVLPAI 302

Query: 305 RAEV 308
              V
Sbjct: 303 VVSV 306


Lambda     K      H
   0.320    0.137    0.391 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 351
Number of extensions: 16
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 384
Length of database: 363
Length adjustment: 30
Effective length of query: 354
Effective length of database: 333
Effective search space:   117882
Effective search space used:   117882
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory